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VIOLIN News
News: Find our publication records by clicking: All vaccine-related journal papers published in He laboratory since 2007 when VIOLIN was initiated (available in PubMed). See more in our publications page.
More news:
- 2/6/2025: VIOLIN vaccine knowledgebase was systematically analyzed for pattern detection, which was published in Front. Cell. Infect. Microbiol today.
- 11/15/2024: A paper titled "Impact of climate change on vaccine responses and inequity", was published in Nature Climate Change.
- 11/8/2024: A paper titled "Assessing acute kidney injury risk after COVID vaccination and infection in a large cohort study" (PMID: 39516206, PMCID: PMC11549351) was published in npj Vaccines. Congratulations!
- 6/19/2024: A paper on empowering standardization of cancer vaccines through ontology (PMID: 38890666, PMCID: PMC11186274) was published on JBMS.
- 4/25/2024: A JBMS paper on ontological representation, modeling, and analysis of parasite vaccines (PMID: 38664818, PMCID: PMC11044459) was published.
- 1/12/2024: Our CanVaxKB cancer vaccine knowledgebase was published in NAR Cancer (PMID: 38204924, PMCID: PMC10776203).
- 12/1/2023: We published a Vaxign-DL BioRxiv paper introducing our Vaxign-DL deep learning program.
- 11/11/2023: Oliver He presented VIOLIN vaccine knowledgebase in the Knowledge Representation and Semantics Working Group Pre-Symposium (KRS-WG-2023) at AMIA 2023, New Orleans.
- 10/20-22/2023: Yuanyi "Penny" Pan and Oliver He attended 2023 OHDSI Symposium, East Brunswick, New Jersey, and presented a poster titled "Harmonization of OMOP vaccine-related vocabularies through the Vaccine Ontology".
- 08/29/2023: Cui, Junguk, and Oliver co-organized the International Workshop on Vaccine and Drug Ontology Studies (VDOS-2023), associated with the ICBO-ONTOBRAS, Brasilia, Brazil, at 08/28-09/01/2023. Our VIOLIN team also presented many papers/studies in VDOS-2023 and the main ICBO-ONTOBRAS conference.
- 02/28/2023: Asiyah presented the OHDSI Vaccine Vocabulary WG Objectives and Key Results (OKR) in the OHDSI community call on Feb 28, 2023.
- 10/31/2022: Asiyah Yu Lin and Oliver He started to co-chair the OHDSI Vaccine Vocabulary Working Group (WG). We proposed for OHDSI to consider adopting the OBO Vaccine Ontology (VO) as the standard representation for vaccines.
- 8/19/2022: A 5-year NIH U24 grant titled "VIOLIN 2.0: Vaccine Information and Ontology LInked kNowledgebase" (U24AI171008) was awarded to MPIs: Drs. Yongqun "Oliver" He (contact), Cui Tao, and Junguk Hur. Congratulations!
- 6/24/2022: Our new COVID-19 vaccine adverse event paper titled "Profiling COVID-19 vaccine adverse events by statistical and ontological analysis of VAERS case reports " was published in Frontiers in Pharmacology.
- 6/21/2022: Oliver presented a talk titled "Ontology Supported Integrative Analysis and Visualization of Vaccine-Induced Pathways and Networks" in 2022 FOCIS Big Data in Immunology workshop.
- 6/2/2022: Our review article titled "COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning" was published in Briefs in Bioinformatics. PMID: 35649389.
- 1/7/2022: Our paper on Cov19VaxKB COVID-19 Vaccine Knowledge Base was published in Vaccine: X. Click Here for paper detail.
- 11/17/2021: Our Vaxign/Vaxign-ML protocol paper is published as a book chapter in Methods in Molecular Biology book series. 15th Vaccine Congress.
- 10/4-6/2021: Oliver He will present the Cov19VaxKB COVID-19 Vaccine Knowledge Base in the 15th Vaccine Congress.
- 6/9/2021: Oliver He will present a talk in the FDA MIDD Immunogenicity Workshop. His talk title is: "COVID-19 vaccine machine learning, ontology modeling, and Cov19VaxKB". See the detailed AGENDA.
- 5/1/2021: Our Vaxign2 vaccine design program paper was published in Nucleic Acid Research : https://doi.org/10.1093/nar/gkab279.
- 4/15/2021: Our Vaxign2 vaccine design program paper was accepted for publication in the Nucleic Acid Research annual Web Server issue.
- 2/18/2021: The vaccine immune factor database VaximmutorDB paper was accepted for publication in Froniters in Immunology. See the VaximmutorDB article on the journal site for more details.
- 2/8/2021: "Reverse Microbiolomics", a new method based on (Vaxign) reverse vaccinology tool, was published and applied to supprot the prediction of autoantigens and virulence factors in dysbiotic gut microbiomes from rheumatoid arthritis patients. See detail in the Reverse Microbiomiics paper in Froniters in Microbiology.
- 12/31/2020: Oliver He lab and Yang Zhang lab collaborated and published "Computational Design of SARS-CoV-2 Spike Glycoproteins to Increase Immunogenicity by T Cell Epitope Engineering" (PMID: 33398234) in Comput Struct Biotechnol J. This paper was previously published in a bioRxiv paper.
- 10/31/2020: In This Week in Virology (TWIV) episoide 677 (title: Does antibody really know what time it is?), Dr. Rich Condit mentioned our VIOLIN vaccine database at the time of 2 hours and 33 min, and provided a positive review.
- 9/19/2020: Anthony Huffman and Oliver He presented in the 9th International Workshop on Vaccine and Drug Ontology Studies (VDOS-2020). Oliver was a co-organizer of this workshop.
- 8/14/2020: Oliver He lab and Yang Zhang lab collaborated and published a bioRxiv paper "Rational Design of SARS-CoV-2 Spike Glycoproteins To Increase Immunogenicity By T Cell Epitope Engineering".
- 7/3/2020: He lab published the paper "COVID-19 Coronavirus Vaccine Design Using Reverse Vaccinology and Machine Learning" (PMID: 32719684) in Frontiers in Immunology. This paper was initially published in the bioRxiv on March 23. Vaxign and Vaxign-ML were used for COVID-19 vaccine design.
- 2/18/2020: Edison's Vaxign-ML machine learning for vaccine design paper published in the journal Bioinformatics, which is also availble in PubMed.
- 12/23/2019: Our paper of using ontology to support classification and study of vaccine responses given different conditions was published.
- 7/29-8/2/2019: Edison Ong and Oliver He attended the 8th International Workshop on Vaccine and Drug Ontology Studies (VDOS-2019), in conjunction with the 8th International Conference on Biomedical Ontology (ICBO). Oliver was a co-organizer of this workshop.
- 6/12/2019: Dr. Oliver He and Dr. Guanming Wu were awarded by NIH a grant entitled "Ontology-supported Integrative Analysis and Visualization of Vaccine-induced Pathways and Networks" (1UH2AI132931-01A1) for a project period of two years (06/12/2019 - 05/31/2021). VaximmutorDB is a big part of the UH2 project. We will improve our VaximmutorDB significantly with the grant support.
- 2014-2019: Continuous VaximmutorDB data collection and annotation.
- 5/28/2019: A collaborative paper of developing a new statistical analysis of vaccine adverse event data was published.
- 1/8/2019: Our Victors virulence factors database paper was published in NAR database issue. This paper introduces the relation between virulence factors and protective vaccine antigens.
- 12/4/2018: Oliver visited Merck Research Laboratories, Rahway, NJ. USA, and presented an invited talk titled "Ontology-based knowledge and data management, integration, and mining to support vaccine and drug R&D".
- 8/10/2018: Oliver He attended the 7th International Workshop on Vaccine and Drug Ontology Studies (VDOS-2018), at August 10, 2018 (Friday), Corvallis, Oregon, USA, in conjunction with the 9th International Conference on Biomedical Ontology (ICBO), August 7-10, 2018. Oliver was a co-organizer of this workshop.
- 4/26/2018: Our paper titled "Ontology-based Meta-Analysis of Animal and Human Adverse Events Associated with Licensed Brucellosis Vaccines" was accepted for publication in Front. Pharmacol.
- 12/2017: Our paper titled "The Ontology of Biological and Clinical Statistics (OBCS)-based statistical method standardization and meta-analysis of host responses to yellow fever vaccines" was published in Quantitative Biology.
- 2/21/2017: We published a Vaxign paper that used Vaxign reverse vaccinonlogy to predict antibiotic resistance determinant-focused Acinetobacter baumannii vaccine candidates.
- 1/25/2017: A study using Vaxign vaccine design program was published in Veterinary Immunology and Immunopathology. This study used Vaxign and a newly developed ranking method to identify and rank African swine fever vaccine candidates.
- 9/13/2017: Edison attended the 6th International Workshop on Vaccine and Drug Ontology Studies (VDOS-2017), Newcastle, UK September 13, 2017, which was in conjunction with the International Conference on Biological Ontology (2017). Oliver was a co-organizer of this workshop.
- 10/6/2016: A PloS One paper was published to study the differential adverse event profiles associated with BCG as a preventive tuberculosis vaccine or therapeutic bladder cancer vaccine using ontology-based VAERS and literature meta-analysis.
- 10/3/2016: A Scientific Reports paper was published to study the adverse events related to the interactions betweeen a hepatitis A vaccine (i.e., Havrix) and a hepatitis B vaccine (i.e., Engerix-B).
- 04/19/2016: Our Vaccination Informed Consent Ontology (VICO) was published in J Biomed Semantics.
- 8/1/2016: The 5th International Workshop on Vaccine and Drug Ontology Studies (VDOS-2016), Corvallis, OR, USA Aug. 1 2016, in conjunction with the Joint International Conference on Biological Ontology and BioCreative (2016). Oliver was a co-organizer of this workshop.
- 04/01/2016: Our Vaxar paper was published in Comparaitve Medicine.
- 9/30/2015: Oliver presented an invited talk titled "Ontology development and applications for clinical and biological adverse event data integration and analysis" at the University of Texas (UT) School of Biomedical Informatics. YouTube video: https://www.youtube.com/watch?v=ucowhfJFW_8.
- 9/28-30/2015: Oliver He attended the 4th Immunology Summit 2015 at Houston, USA. As a keynote speaker, on 9/28/2015 he presented a talk titled "Rational vaccine design using reverse vaccinology, database data analysis, and literature mining".
- 9/4/2015: Oliver presented an invited talk titled "Applications of Bioinformatics in Vaccine and Host-Pathogen Interaction Research. Invited departmental research seminar presentation" in the Department of Comparative Pathobiology College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA.
- 7/27-30/2015: Oliver He attended the VDOS-2015 workshop and ICBO-2015 conference held at Lisbon, Portugal, on July 27-30. Oliver co-organized the VDOS-2015 workshop and he presented two full length articles as well. In the general ICBO-2015 conference, Oliver presented two posters and two software demostrations. See the details of these articles, posters, and demos, see the Publication page.
- 7/23/2015: Our Vaxvec paper was accepted by the journal Vaccine.
- 10/22/2014: As shown on this web page, Oliver will present a Special Topic Lecture titled "Database Development and Bioinformatics Analysis of Laboratory Animal Responses to Vaccinations" on the 65th AALAS national meeting at San Antonio, Texas, on Oct 22 (Wed), 2014. AALAS represents for the American Association for Laboratory Animal Science, an association of professionals aimed for advancing responsible laboratory animal care and use to benefit people and animals.
- 10/06-10/09/2014: Oliver will attend the International Conference on Biomedical Ontologies (ICBO 2014) conference in Houston, TX. He is also a co-organizer of the Vaccine and Drug Ontology Studies (VDOS 2014) workshop to be held on Oct 7, 2014, prior to the general meeting of the ICBO-2014.
- 08/12/2014: Oliver spoke at the Cambridge Healthtech Institute’s Ninth Annual "Novel Vaccines" conference, as part of the ImVacS (The Immunotherapies and Vaccine Summit), Boston, MA. His presentation talk is: "Databases and in silico Tools for Vaccine Design". VIOLIN is a focus of his talk.
- 6/7/2014: Oliver's Expert Reviews in Vaccines paper (PMID: 24909153) was published. In this paper, Oliver introduced VIOLIN and how Vaccine Ontology and other ontologies are able to help vaccine efficacy and vaccine adverse event research. He also proposed a so-called “One Network (OneNet) Theory of Life” and ontology-based strategies to study the OneNet interaction network mechanisms of individual organisms including humans.
- 3/27/2014: Announced the VaximmutorDB project. This project focuses on annotation and analysis of vaccine-induced immune factor responses.
- 3/19/2014: The full content of the supplement "ICoVax 2013" were released at http://www.biomedcentral.com/bmcbioinformatics/supplements/15/S4.
- 1/2014: VIOLIN update paper was published in NAR. PMID: 24259431.
- 10/26/2013: “The 3rd ISV Pre-conference Computational Vaccinology Workshop” (ICoVax 2013: http://www.violinet.org/icovax2013/). ICoVax 2013 was a satellite workshop of the 7th Vaccine & ISV Annual Global Congress (http://www.vaccinecongress.com/). ICoVax 2012 was held on Oct 26, 2013, at Barcelona, Spain. Oliver is a co-organizer and co-chair of the conference.
- 7/29-31/2013: Oliver presented a talk on the Vaccines-2013, with the talk title "Applications of the Vaccine Ontology (VO) in vaccine data integration and computer-assisted automated reasoning".
- 7/7/2013: The workshop “Vaccine and Drug Ontology Studies (VDOS-2013)”, International Conference on Biomedical Ontologies (ICBO), Montreal, Qc, Canada, July 7, 2013. URL: http://informatics.mayo.edu/CNTRO/index.php/Events/VDOS_2013. Oliver was a co-organizer and co-chair of the conference. This workshop occurred before the ICBO-2013. Oliver and Asiyah each presented an oral presentaiton.
- 3/13/2013: Oliver presented a talk at FDA with the title "The Ontology of Adverse Events". This visit was invited and organized by Drs. Darrell Abernethy and Jane Bai at the FDA Office of Clinical Pharmacology (OCP).
- 2/11-12/2013: Oliver will attend the CTSA Ontology Workshop in Orlando, FL. He will present the Vaccine Ontology (VO) in the workshop.
- 12/20/2012: A thematic series titled Vaccine and drug ontology in the study of mechanism and effect (VDOSME) was published in the Journal of Biomedical Semantics (JBMS). The thematic series was co-organized by Oliver. VO-related papers were presented. Also, check a related BioMed Central blog.
- 10/24/2012: Allen and Oliver's algorithm for predicting eluted protein epitopes was announced by Vladmir Brusic as one of the winners in the 2nd Machine Learning Competition in Immunology 2012.
- 10/16/2012:Oliver presented an oral presentation in the general Vaccine & ISV Annual Global Congress. His presentation title is: Systematic annotation and analysis of "virmugens" - virulence factors whose mutants can be used as live attenuated vaccines.
- 10/13/2012: Oliver co-organized the 2nd ISV Pre-conference Computational Vaccinology Workshop (ICoVax 2012), a satellite workshop of the general Vaccine & ISV Annual Global Congress. Oliver also presented an oral presentation. Allen also attended the workshop and presented Vaxign software demo.
- 7/21/2012: Oliver co-organized an ICBO 2012 workshop entitled "Vaccine and Drug Ontology in the Study of Mechanism and Effect" (VDOSME 2012), in the Medical University of Graz, Austria. Oliver presented two talks in the workshop as well. Here is the workshop final program.
- 5/2/2012: Oliver presented a Webinar presentation in NCBO Webinar Series. His presentation title is: "Vaccine Ontology (VO) and its application in literature mining of vaccine-gene interaction networks".
- 1/6/2012: Oliver and Allen attended the "African Swine Fever Reverse Vaccinology Project" kickoff meeting in the National Center for Foreign Animal and Zoonotic Disease Defense (FAZD) in Texas. In this meeting, Allen presented our Vaxign vaccine candidate prediction program, and Oliver introduced the prediction results using the Vaxign reverse vaccinology tool.
- 10/17-19/2011: Oliver attended the 5th Annual Vaccine Renaissance Conference (Vax-Ren-5) at Providence, RI, USA. He presented a talk "Genome-wide vaccine target prediction based on Vaxign reverse vaccinology".
- 10/2-4/2011: Oliver and Allen presented two posters in the 5th Vaccine and ISV Annual Global Congress in Seattle. Oliver's poster title is "VIOLIN: an integrative vaccine research database and analysis system". Allen's poster title is: "Bioinformatics analysis of protective antigens in manually curated Protegen database".
- 10/1/2011: Oliver presented a talk "Genome-wide vaccine target prediction using Vaxign reverse vaccinology" in the 1st Computational Vaccinology workshop prior to the 5th Vaccine and ISV Annual Global Congress. Oliver and Allen has also organized a 1.5-hour Vaxign hands-on exercise.
- 6/20/2011: A comprehensive 26-page review article titled "Emerging Vaccine Informatics" in the Journal of Biomedicine and Biotechnology 2010 special issue on vaccine informatics was published. Oliver is a co-author of this article. This review also introduces VIOLIN and VO.
- 4/23-25/2011: Oliver attended the BIT 3rd World Vaccine Congress. He gave a talk on Vaxign vaccine design and co-chaired the section "Section 2-2-1: Bioinformatics, Antigen Design, and Vaccine Development".
- 12/8-9/2010: Oliver, Allen, and Asiyah (Yu Lin) attended the IDO Workshop 2010. Asiyah presented Brucellosis Ontology, Allen presented OntoBee, and Oliver updated the development of Vaccine Ontology (VO).
- 9/28/2010: A new paper about the application of VIOLIN in analysis/prediction of Brucella vaccines and vaccine targets was published. The PubMed ID is: 20875156.
- 9/26-28/2010: Oliver He attended InCoB2010 in Tokyo, Japan. He presented a talk on how to use VIOLIN to analyze and predict Brucella vaccines and vaccine targets.
- 7/9-13/2010: Oliver and Sira attended the Bio-Ontologies 2010 meeting, which is an ISMB SIG meeting. Arzucan Ozgur and Junguk Hur also presented research out of the collaborations between them and He Lab. In total, two oral presentations and two poster presentations were given by He Lab in the conference.
- 3/22-25/2010: Allen Xiang attended the OBI Spring 2010 Workshop at Vancouver, Canada. He presented a use case on vaccine protection investigation using ontology (OBI and VO)-based ANOVA analysis of literature mined data.
- 11/10-12/2009: Dr. Oliver He and Allen Xiang attended the “UTMB Sealy Center for Vaccine Development Symposium” in Galveston, Texas. Dr. He presented a talk in how to use VIOLIN and VO to analyze Brucella vaccines (http://www.utmb.edu/scvd/2009Symposium.pdf).
- 9/21/2009: An Notice of Award (NoA) was issued by NIH-NIAID to officially award Oliver He (PI) and his team and collaborators an R01 grant with the title: "Ontology-based Information Network to Support Vaccine Research" (Grant Number: R01AI081062). This is a four-year grant with an aim to develop VO and apply it for ontology-based literature mining and analysis of vaccine-induced protective immune networks.
- 7/24-26/2009: Oliver and two lab members (Allen and Sira) attended the 1st International Conference on Biomedical Ontology (ICBO) conference in Buffalo, NY. Two posters and one software demo were presented, all related to Vaccine Ontology (VO) development and application. One poster is introduction of VO, the other is on using VO for literature mining. The software demo is about OntoFox, which a side project derived from the VO development. OntoFox is used for VO development. More details can be seen in the I CBO proceedings.
- 5/17-21/2009: Oliver attended the 109th ASM General Meeting in Philadelphia, PA. He presented a poster titled "Development of a Community-based Vaccine Ontology".
- 2/2-6/2009: Oliver attended the OBI 2009 Vancouver Workshop. Oliver discussed with the OBI development team on how to improving VO with the help from OBI and how to update OBI using vaccine-related terms and term relationships. Oliver presented a talk to discuss the relationships between VO and OBI. Oliver has also joined the OBI Consortium and represents the vaccine community in the OBI development.
- 12/07-09/2008: Dr. Oliver He presented an oral presentation in the 2nd Vaccine Congress organized by the International Society for Vaccines (ISV) and the journal Vaccine. His presentation title is: "Vaxign: a web-based vaccine target design program for reverse vaccinology". In his talk, Oliver focused on introducing the first web-based vaccine design system based on the reverse vaccinology concept originally pioneered by Dr. Rino Rappuoli. Oliver received very positive feedback and encouragements from the vaccine community, including Dr. Rappuoli, the founder of this novel approach for vaccine development. After Dr. He's talk, many groups contacted him for instructions and possible collaborations.
- 09/16-17/2008: Oliver He attended the Infectious Disease Ontology (IDO) 2008 workshop. In the workshop Oliver presented a talk on the progress of the Vaccine Ontology.
- Aug 14, 2008: Dr. Oliver He gave a speaker presentation in the Cambridge Healthtech Institute (CHI) conference "Novel Vaccines: Bridging Research, Development & Production". His presentation title is "An Ontology-based Information Network to Support Vaccine Research".
- July 19, 2008: We presented the VIOLIN and Vaccine Ontology project in ISMB2008 and here is a PDF version.
- April 12-13, 2008: Both Dr. Oliver He and Zuoshuang (Allen) Xiang attended the training course by Dr. Barry Smith: "An Introduction to Biomedical Ontology" in Buffalo, NY, USA. Dr. Smith introduced ontology with special reference to applications in biomedical research, including Vaccine Ontology.
- March 19, 2008: Dr. Oliver He was awarded to give a speaker presentation in August 2008 in the Cambridge Healthtech Institute (CHI) conference "Novel Vaccines: Bridging Research, Development & Production", which is part of the Immunotherapeutics& Vaccine Summit--ImVacS. His presentation title is "An Ontology-based Information Network to Support Vaccine Research".
- Jan 10, 2008: VIOLIN Wiki was created. The collaborative effort of Vaccine Ontology development was described in the Wiki site.
- Nov 19, 2007: The VIOLIN manuscript was published in the Nucleic Acid Research Database issue as an Epub version (PMID: 18025042).
- Mar 23, 2007: VIOLIN website was online and had its first show.
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